User: Dr Gyorffy Balazs

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Posts by Dr Gyorffy Balazs

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vsn on vsn
... Hi All! I want to merge the two different microarray datasets, one was VSN normalized and the other one quantile-normalized. Can I use a second VSN normalization? Any other normalization / related literature? Thanks: Balazs ------------------------- Balázs GYÖRFFY MD, PhD Research Laboratory ...
microarray normalization written 8.2 years ago by Dr Gyorffy Balazs320 • updated 8.2 years ago by Sean Davis21k
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rawQ Affymetrix
... Dear All, we would like to use the computeRawQ function, but the documentation is very scarce: Arguments fname                    character string with the filename of the GeneChip intensity                    vector of intensities for the GeneChip probe.index             vector of indices for eac ...
written 9.7 years ago by Dr Gyorffy Balazs320
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MAS5 to selected average
... Hi! MAS5 normalizes to different averages when using HGU133A (to 800) and HGU133Aplus2 (to 1500) chips. Can I set the target average during normalization? Thanks Balazs [[alternative HTML version deleted]] ...
hgu133a written 10.5 years ago by Dr Gyorffy Balazs320
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how to match tables
... Hi All, This would be extremely easy in Access, but should be manageable in R too :-) I have two tables, which are the annotation files for two platforms. I have one common identifier, the ”probenames”, which is used in both tables. I would like combine table 1 and table 2 into table 3. The †...
annotation written 11.4 years ago by Dr Gyorffy Balazs320 • updated 11.4 years ago by Sean Davis21k
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row maximum
... Hi All,I have a very simple problem: I have a table. How can I add the maximal value of each row in a new column to the table? (I tried "apply(table, 1, max)" but without success)ThanksBalazs __________________________________________________________ Dem pfiffigeren Posteingang. ...
written 11.4 years ago by Dr Gyorffy Balazs320 • updated 11.4 years ago by Steve Lianoglou12k
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select genes from a table above a threshold
... Hi All! I have a table. Rows: genes - one gene is represented by several probes, colums: samples. Values: expression ratios. I would like to get the values for all samples and all probes for those genes, which have an expression ratio higher that 2 in at least 2 different measurements. (Thus thes ...
probe written 11.6 years ago by Dr Gyorffy Balazs320 • updated 11.6 years ago by Thomas Girke1.7k
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computation of average of all probes but not the actual
... Hi All, Lets say, we have a table, and want to divide the values with the row averages: mytable <- array(1:20, dim=c(4,5)) averages <- apply(mytable, 1, mean) result <- mytable/averages How can I make this in a way in which each probe is divided by an average which was calulated by all p ...
probe written 11.6 years ago by Dr Gyorffy Balazs320 • updated 11.6 years ago by Hervé Pagès ♦♦ 14k
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splicing in Affymetrix
... Hi All! I have a table (see attached shortened example). Here the columns represent the samples (two here) and the rows the probe pairs. 16 probe pair represent a probe set (however, some probe sets contain only 11 or 14 probe pairs!). I would like to divide the probe pairs by the average of a pr ...
go probe written 11.6 years ago by Dr Gyorffy Balazs320 • updated 11.6 years ago by Christos Hatzis110
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exprs2excel problem
... Hi All! I got long ago used to R 2.3.1, and yesterday I upgraded to the current vesion (R 2.6.2). And of course I run into a major problem: the exprs2excel command is not functioning any more. I receive following error message after MAS5 normalization: > Myproject.raw<-ReadAffy() > Myproj ...
written 11.7 years ago by Dr Gyorffy Balazs320 • updated 11.7 years ago by James W. MacDonald52k
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brb arraytools and excel 2007
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071004/ 380718fd/attachment.pl ...
written 12.2 years ago by Dr Gyorffy Balazs320 • updated 12.2 years ago by Sean Davis21k

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Popular Question 8.2 years ago, created a question with more than 1,000 views. For converting GEO soft files to MS excel files

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