Dear Francois, Thank you very much for reporting these problems, I will try to fix them as soon as possible. I have never noticed the weird spatial plots you are mentioning on my test slides; could you please send me the file you are using so that I can see what is going on? Regards, Agnes -----Original Message----- From: Francois Pepin [mailto:fpepin@cs.mcgill.ca] Sent: Friday, December 02, 2005 4:06 PM To: BioClist Cc: Paquet, Agnes; Jean Yee Hwa Yang Subject: bugs in arrayQuality and marray Hi everyone, I've hit a couple of bugs while trying out arrayQuality (downloaded from ucsf site, they have an earlier version than bioconductor) for my Agilent arrays. read.Agilent, from the marray package, is ignoring the 'path' parameter when 'fnames' is given: if (is.null(fnames)) { ... } else fullnames <- fnames The readAgilent function, from the arrayQuality package, has problems with the skip parameter. First of all, it is completely ignored: skip <- grep("gMedianSignal", y)[1] Then lower down, it is incorrectly offset by +1: dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + 1, quote = quote, ...) which means that the first gene is skipped (which then cause problems because dimensions are not of the same). Then maPrintTip in marray is confused with how Agilent probes are positioned and seems to think that there are twice as many probes as there are. Doing a print tip-based normalization doesn't make much sense in this case (only 1 print tip is present), but it did end up making the code crash. This can be fixed by specifying norm='l' (if loess normalization is wanted) in the agQuality. I think that should be the default in agQuality and change (in agQuality): defs <- list(norm = "p") to defs <- list(norm = "l") As a note, the diagnostic spatial images being produced are not correct either. It produces 4 copies of the image rather than a single one. I've attached a the output from a truly horrible array we have where it's obvious. I assume this is again due to the awkward way Agilent has to place its spots. > sessionInfo() R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu attached base packages: [1] "grid" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: arrayQuality RColorBrewer gridBase hexbin colorspace convert "1.6.2" "0.2-3" "0.4-1" "1.4.0" "0.9" "1.4.0" Biobase marray limma "1.8.0" "1.8.0" "2.3.7" Francois

Hi everyone, I've hit a couple of bugs while trying out arrayQuality (downloaded from ucsf site, they have an earlier version than bioconductor) for my Agilent arrays. read.Agilent, from the marray package, is ignoring the 'path' parameter when 'fnames' is given: if (is.null(fnames)) { ... } else fullnames <- fnames The readAgilent function, from the arrayQuality package, has problems with the skip parameter. First of all, it is completely ignored: skip <- grep("gMedianSignal", y)[1] Then lower down, it is incorrectly offset by +1: dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + 1, quote = quote, ...) which means that the first gene is skipped (which then cause problems because dimensions are not of the same). Then maPrintTip in marray is confused with how Agilent probes are positioned and seems to think that there are twice as many probes as there are. Doing a print tip-based normalization doesn't make much sense in this case (only 1 print tip is present), but it did end up making the code crash. This can be fixed by specifying norm='l' (if loess normalization is wanted) in the agQuality. I think that should be the default in agQuality and change (in agQuality): defs <- list(norm = "p") to defs <- list(norm = "l") As a note, the diagnostic spatial images being produced are not correct either. It produces 4 copies of the image rather than a single one. I've attached a the output from a truly horrible array we have where it's obvious. I assume this is again due to the awkward way Agilent has to place its spots. > sessionInfo() R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu attached base packages: [1] "grid" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: arrayQuality RColorBrewer gridBase hexbin colorspace convert "1.6.2" "0.2-3" "0.4-1" "1.4.0" "0.9" "1.4.0" Biobase marray limma "1.8.0" "1.8.0" "2.3.7" Francois -------------- next part -------------- A non-text attachment was scrubbed... Name: diagPlot.US22502628_251239112296_S01_A01.png Type: image/png Size: 130019 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20051202 /c2a01c28/diagPlot.US22502628_251239112296_S01_A01.png

Hi everyone, (note to moderators: please reject my previous message, I'm resending with a link to the file instead of an attachment). I've hit a couple of bugs while trying out arrayQuality (downloaded from ucsf site, they have an earlier version than bioconductor) for my Agilent arrays. read.Agilent, from the marray package, is ignoring the 'path' parameter when 'fnames' is given: if (is.null(fnames)) { ... } else fullnames <- fnames The readAgilent function, from the arrayQuality package, has problems with the skip parameter. First of all, it is completely ignored: skip <- grep("gMedianSignal", y)[1] Then lower down, it is incorrectly offset by +1: dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + 1, quote = quote, ...) which means that the first gene is skipped (which then cause problems because dimensions are not of the same). Then maPrintTip in marray is confused with how Agilent probes are positioned and seems to think that there are twice as many probes as there are. Doing a print tip-based normalization doesn't make much sense in this case (only 1 print tip is present), but it did end up making the code crash. This can be fixed by specifying norm='l' (if loess normalization is wanted) in the agQuality. I think that should be the default in agQuality and change (in agQuality): defs <- list(norm = "p") to defs <- list(norm = "l") As a note, the diagnostic spatial images being produced are not correct either. It produces 4 copies of the image rather than a single one. I've put at put the output from a truly horrible array we have where it's obvious on my website http://www.mcb.mcgill.ca/~francois/diagPlot.US22502628_251239112296_S0 1_A01.png . I assume this is again due to the awkward way Agilent has to place its spots. > sessionInfo() R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu attached base packages: [1] "grid" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: arrayQuality RColorBrewer gridBase hexbin colorspace convert "1.6.2" "0.2-3" "0.4-1" "1.4.0" "0.9" "1.4.0" Biobase marray limma "1.8.0" "1.8.0" "2.3.7" Francois

Hi Francois, I have started looking at the problems you reported last week. From a visual inspection of your image processing output file, I think that the problem comes from the way Agilent image processing software is managing the orange packing format. Agilent image analysis software is keeping the orange packing format in the output file (which is different from other software package like GenePix) is a way that is not accounted for in marray. The layout of the array in the file looks something like: Feature Num Row Col 1 1 1 2 1 3 3 1 5... 215 1 429 216 2 2 217 2 4 218 2 6 The real layout of your array should be 215 columns by 206 rows, but marray is reading 430 columns by 206, creating an object with twice as many spots, as you reported... I will forward this problem to Jean Yang, who is the maintainer of marray, so that she can address this issue. Thank you very much for reporting this, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Francois Pepin Sent: Friday, December 02, 2005 4:14 PM To: BioClist Subject: [BioC] bugs in arrayQuality and marray Hi everyone, (note to moderators: please reject my previous message, I'm resending with a link to the file instead of an attachment). I've hit a couple of bugs while trying out arrayQuality (downloaded from ucsf site, they have an earlier version than bioconductor) for my Agilent arrays. read.Agilent, from the marray package, is ignoring the 'path' parameter when 'fnames' is given: if (is.null(fnames)) { ... } else fullnames <- fnames The readAgilent function, from the arrayQuality package, has problems with the skip parameter. First of all, it is completely ignored: skip <- grep("gMedianSignal", y)[1] Then lower down, it is incorrectly offset by +1: dat <- scan(f, quiet = TRUE, what = h, sep = sep, skip = skip + 1, quote = quote, ...) which means that the first gene is skipped (which then cause problems because dimensions are not of the same). Then maPrintTip in marray is confused with how Agilent probes are positioned and seems to think that there are twice as many probes as there are. Doing a print tip-based normalization doesn't make much sense in this case (only 1 print tip is present), but it did end up making the code crash. This can be fixed by specifying norm='l' (if loess normalization is wanted) in the agQuality. I think that should be the default in agQuality and change (in agQuality): defs <- list(norm = "p") to defs <- list(norm = "l") As a note, the diagnostic spatial images being produced are not correct either. It produces 4 copies of the image rather than a single one. I've put at put the output from a truly horrible array we have where it's obvious on my website http://www.mcb.mcgill.ca/~francois/diagPlot.US22502628_251239112296_S0 1_ A01.png . I assume this is again due to the awkward way Agilent has to place its spots. > sessionInfo() R version 2.2.0, 2005-10-06, x86_64-redhat-linux-gnu attached base packages: [1] "grid" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: arrayQuality RColorBrewer gridBase hexbin colorspace convert "1.6.2" "0.2-3" "0.4-1" "1.4.0" "0.9" "1.4.0" Biobase marray limma "1.8.0" "1.8.0" "2.3.7" Francois _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor