similar to: limma function problem

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of

Hi, It's unfortunate that with recent revisions of R 2.13 (this appeared in revision 54640, March 2), 'R CMD build' now removes empty dirs in the package. People might have good reasons for having empty dirs in their packages. For example, in Bioconductor, we have some tools to automatically generate annotation packages and those tools are implemented in software packages that use

Greetings ~ I need some assistance determining an appropriate approach to analyzing multivariate binary response data, and how to do it in R. The setting: Data from an assay, wherein 6-hours-post-fertilization zebrafish embryos (n=20, say) are exposed in a vial to a chemical (replicated 3 times, say), and 5 days later observed for the presence/absence (1/0) of defects in several organ systems

Dear all, I am currently analyzing a set of arrays hybe on the lattest affy Drosophila 2.0 GeneChip. I am trying to run simple annaffy analysis but can¹t find what is the name of the annotation file I need to use. Here is the output of the AffyBatch object I am using: > expData AffyBatch object size of arrays=732x732 features (16749 kb) cdf=Drosophila_2 (18952 affyids) number of samples=4

I am trying to drop rows of a dataframe based on values of the column PID, but my strategy is not working. I hope someoen can tell me what I am doing incorrectly. # Values of PID column > jdata[,"PID"] [1] 16608 16613 16355 16378 16371 16280 16211 16169 16025 11595 15883 15682 15617 15615 15212 14862 16539 [18] 12063 16755 16720 16400 16257 16209 16200 16144 11598 13594 15419 15589

Hi, I have downloaded around 60GB package repositories of bioconductor to use it locally and to set up mirror at my university site. I have installed the mirror with rsync command and able to access also. Now I have to set a cron job for its daily updating from bioconductor website. How should I do it? I know rsync have to be used but I don't know the proper syntax. I request to send

Hi All, Whenever i try to start FOP using script ./op_panel_redhat.sh start given in directory /usr/local/op_panel-snapshot/init I got the following error: Starting Flash Operator Panel: execvp: No such file or directory [FAILED] Please let me know the reason for this. Thanks in Advance With Regards, newbie

Hi, I have 15 CEL files of Affymetrix platform from GEO. Title of experiment is : Ecoli_ASv2 Affymetrix E. coli Antisense Genome Array. I am looking for the package available in R for this array for annotation. I have already tried doing annotation from packages like org.EcK12.eg.db but I don't got the success. Is any other package in the form of database available for E.coli for

Hi, I m not able to plot normalized data(normalization by rma) using boxplot. I don't know why? basically, object(formed of normalized data) belong to ExpressionSet class. It is showing error Error in x[!xna] : object of type 'S4' is not subsettable In addition: Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(x) : is.na()

Hi All, I am getting following error when i start AsterFax: Please help me to solve this issue: [root at prefroam asterfax]# ./asterfax.sh log4j: Threshold ="null". log4j: Retreiving an instance of org.apache.log4j.Logger. log4j: Setting [au.com.noojee.asterfax] additivity to [false]. log4j: Level value for au.com.noojee.asterfax is [DEBUG]. log4j:

I'd like to expand the following data to perform a daily time series. It should cover from '2012-07-01' to '2012-10-06' with the values I actually have being the mean from one point measurement to another. Does anyone has a clue to perform this task. structure(list(Date.beg = structure(c(15635, 15617, 15615, 15610, 15609, 15605, 15604, 15601, 15593, 15593, 15586, 15581,

Hi Friends, Am facing the serious issue in outlook 2016. When i tried to configure the email in outlook 2016 it's asking encrypted connection and checked automatically and if not available then it showing unencrypted. but finally unable to configure the email account in outlook 2016 and not permitted. Do i need to update any in the server. Am using COS 6 32 and 64 bit servers with

hi, i try to use dovecot lda with postfix virtual delivery, but i've got error. the maildirs are created ie: new/, tmp/, curr/, dovecot.index, dovecot.index.log, .dovecot.lda-dupes. but the mail is not placed into it and got and error: "save failed to INBOX". what can be the reason? thank you for your help in advance. yours. --------------------------------- # ls -ald /var/vmail/

I hate it when I crash my email server. Here's what tailing /var/log/qmail/qmail-smtp/current gives me: [root at toast jack]# tail /var/log/qmail/qmail-smtpd/current @400000004e9ddbd031610f54 tcpserver: status: 0/20 @400000004e9ddbd72c767c04 tcpserver: status: 1/20 @400000004e9ddbd72c7ab60c tcpserver: pid 12039 from 210.76.164.235 @400000004e9ddbd739a20d1c tcpserver: ok 12039