search for: affx

...irix6.5 system mips, irix6.5 status major 1 minor 5.0 year 2002 month 04 day 29 language R > test3 sj030110 sj030111 sj030112 control.ppm AFFX-DapX-M_at 216 236 227 13.3 AFFX-DapX-5_at 97 114 108 6.7 AFFX-CreX-5_at 1107 1021 1661 166.7 AFFX-BioB-5_at 595 511 772 83.3 AFFX-BioDn-3_at 3505 3059 4646 666.7 AFFX-BioB-3_at 2691...

...ot; attribue in read.table and still make the colnames and coldata point to the same col#. Please suggest a solution. Thanks, Vasu. -------------- next part -------------- 14A_U133A_StatPairs 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403.0 409.3 611.5 569.2 536.6 580.2 AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956.0 AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6 AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 AFFX-BioC-3_at 1574.5 1273.0 1484.6 1321.2 1474.7 1774.1 AFFX-BioDn-5_at 2333.7 1796.8 24...

...ot; attribue in read.table and still make the colnames and coldata point to the same col#. Please suggest a solution. Thanks, Vasu. -------------- next part -------------- 14A_U133A_StatPairs 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403.0 409.3 611.5 569.2 536.6 580.2 AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956.0 AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6 AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 AFFX-BioC-3_at 1574.5 1273.0 1484.6 1321.2 1474.7 1774.1 AFFX-BioDn-5_at 2333.7 1796.8 24...

...JT 9.07764840614892 210999_s_at JT 9.00219110130877 212284_x_at JT 8.62193952504277 203752_s_at JT 8.69193736253539 203574_at JT 8.41492571590263 219629_at JT 8.19111292436667 201473_at JT 8.035082989931 210592_s_at JT 8.00639829720742 200768_s_at JT 7.88012483915651 201565_s_at JT 7.89885432096935 AFFX-r2-P1-cre-3_at JT 7.86490927895639 202014_at JT 7.69345791769434 212671_s_at JT -7.43350555284605 203395_s_at JT 7.51127977823914 208980_s_at JT 7.52175408445448 207783_x_at JT 7.31954223019292 215446_s_at JT -6.28236730203077 203034_s_at JT 7.24582647671987 211943_x_at JT 7.22247828112639 203974_a...

...ng to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_5_at ratio actin3/actinM AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_M_f_at ratio gapdh3/gapdh5 AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_5_at ratio...

...8.62193952504277 blue 7 203752_s_at JT 8.69193736253539 green 8 203574_at JT 8.41492571590263 blue 9 219629_at JT 8.19111292436667 blue 10 201473_at JT 8.035082989931 green 11 210592_s_at JT 8.00639829720742 green 12 200768_s_at JT 7.88012483915651 green 13 201565_s_at JT 7.89885432096935 green 14 AFFX-r2-P1-cre-3_at JT 7.86490927895639 blue 15 202014_at JT 7.69345791769434 green 16 212671_s_at JT -7.43350555284605 green 17 203395_s_at JT 7.51127977823914 blue 18 208980_s_at JT 7.52175408445448 blue 19 207783_x_at JT 7.31954223019292 blue 20 215446_s_at JT -6.28236730203077 green 21 203034_s_at J...

...ven below to see if any gene(column 1 stands for gene names) is differentially expressed after subjecting it to the 6 different experiments(columns 2 to 7 are experiments). Gene 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403 409.3 611.5 569.2 536.6 580.2 AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956 AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6 AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 AFFX-BioC-3_at 1574.5 1273 1484.6 1321.2 1474.7 1774.1 AFFX-Bio...

I have a data frame which has the following data. data<-read.table("table.txt",header=TRUE) data X14A_U133A_StatPairs X14A_U133A_Detection X14B_U133A_Signal 1 AFFX-BioB-5_at 403.0 409.3 2 AFFX-BioB-M_at 757.3 574.4 3 AFFX-BioB-3_at 284.4 327.3 4 AFFX-BioC-5_at 2314.2 1685.3 5 AFFX-BioC-3_at 1574.5 1273.0 6...

Thanks a lot, James!! The problem is fixed. On the version 1.4.0 Mac/darwin (the latest available version for this system) the function read.table (which is called from read.delim etc., too) has the bug you explained. Inserting the row nlines <- nlines+1 after lines <- c(lines, line) removes this bug. M. On Friday, February 22, 2002, at 02:33 PM, james.holtman at convergys.com

...reads data without any error Now if I use edit(mydata) It shows only 3916 entries, whereas the actual file contains 7129 entries) My data is something like Gene Description Gene Accession Number 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 34 35 36 37 38 28 29 30 31 32 33 AFFX-BioB-5_at (endogenous control) AFFX-BioB-5_at -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165 -67 -92 -113 -107 -117 -476 -81 -44 17 -144 -247 -74 -120 -81 -112 -273 -20 7 -213 -25 -72 -4 15 -318 -32 -124 -135 So it seems R is truncating the data. How can I load the complete file? Thanks in advan...

...str(svm_num_mat) num [1:10, 1:12340] 13.1 13.1 13.1 13.1 13.0 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:10] "rma_log2_con_sample_1" "rma_log2_con_sample_2" "rma_log2_con_sample_3" "rma_log2_con_sample_4" ... ..$ : chr [1:12340] "AFFX-HSAC07/X00351_3_at" "AFFX-HSAC07/X00351_5_at" "AFFX-HSAC07/X00351_M_at" "AFFX-HUMGAPDH/M33197_3_at" ... and the class labels -- > str(m.cl.f) Factor w/ 2 levels "-1","1": 2 2 2 2 2 1 1 1 1 1 > > m.cl.f [1] 1 1 1 1 1 -1 -1 -1...

Hi, I use write.table() to write a file to an external xls file. the column names left-shift one position in output file. I check with col.names() row.names(), the file is fine. How to prevent the shifting? I71 I111 I304 I307 I305 I306 I114 I72 AFFX-BioB-5_at 6.66435 6.787807 5.335962 5.250163 6.47423 5.882104 5.965109 6.591687195 AFFX-BioB-M_at 6.163227 5.965427 4.665569 2.743531 6.097244 5.77137 5.113683 6.314003982 Thanks, Johnny [[alternative HTML version deleted]]

.../biocLite.R") biocLite("Biobase") > library("Biobase") > data(sample.ExpressionSet) > class(sample.ExpressionSet) [1] "ExpressionSet" attr(,"package") [1] "Biobase" > z <- featureNames(sample.ExpressionSet) > z[1:2] [1] "AFFX-MurIL2_at" "AFFX-MurIL10_at" > ?featureNames(sample.ExpressionSet) Warning message: no method defined for function 'featureNames' and signature 'object = "missing"' in: .helpForCall(e1Expr, parent.frame()) Error in .helpForCall(e1Expr, parent.frame()) :...

...t;) > >> library("Biobase") >> data(sample.ExpressionSet) >> class(sample.ExpressionSet) > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" >> z <- featureNames(sample.ExpressionSet) >> z[1:2] > [1] "AFFX-MurIL2_at" "AFFX-MurIL10_at" >> ?featureNames(sample.ExpressionSet) > Warning message: > no method defined for function 'featureNames' and signature 'object = "missing"' in: .helpForCall(e1Expr, parent.frame()) > Error in .helpForCall(e1Expr...

Dear R user, I am trying to convert the contents of a date.frame to a matrix. Since there are negative values in the date.frame, when I use data.matrix(x, rownames.force = NA), the resulting matrix is not the same as the original one. Basically I think R treats the numbers in the date.frame as character and converts it to corresponding numerics. Any idea on this issue? Many Thanks, Hongyuan

...pressionSet (storageMode: lockedEnvironment) assayData: 500 features, 7 samples element names: exprs, se.exprs phenoData sampleNames: C, F, ..., X (7 total) varLabels and varMetadata description: sex: Female/Male type: Case/Control score: Testing Score featureData featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: hgu95av2 # what I would like to allow in use: (subset2 = subset(expressionSet, sex=="Male", score > 0.75) # note the...

Dear all, Is there a way with Bioconductor in which I can convert such EnSemBL probe names into the standard gene names? AFFX-M27830_5_at AFFX-M27830_M_at ENSG00000000003_at ENSG00000000005_at ENSG00000000419_at - Gundala Viswanath Jakarta - Indonesia

...263 (gdb) p i $7 = 22839 (gdb) p idx $8 = 22840 Both rm and lapply are needed to trigger the fault; an R level gc() before the final line 'cures' the fault (and the valgind complaint). The data file is available (with free registration) at https://www.affymetrix.com/support/file_download.affx?onloadforward=/analysis/downloads/na22/ivt/Barley1.na22.annot.csv.zip Martin -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

...143262 3.6517 0.08019 . Residuals 12 470776 39231 --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 > temp <- lapply(anovaresults, function(x) { x["Pr(>F)"][1:3,] }) > length(temp) [1] 22690 > temp[1] $"AFFX-BioB-5_at" 1 2 3 0.63906707 0.13865289 0.08018914 > gc(verbose=TRUE) Garbage collection 62 = 23+6+33 (level 2) ... 1430471 cons cells free (28%) 17.4 Mbytes of heap free (32%) used (Mb) gc trigger (Mb) Ncells 3249183 86.8 4953636 132.3 Vcells 4749...